4B8C

nuclease module of the yeast Ccr4-Not complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


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Literature

Architecture of the Nuclease Module of the Yeast Ccr4-not Complex: The not1-Caf1-Ccr4 Interaction.

Basquin, J.Roudko, V.V.Rode, M.Basquin, C.Seraphin, B.Conti, E.

(2012) Mol Cell 48: 207

  • DOI: 10.1016/j.molcel.2012.08.014
  • Primary Citation of Related Structures:  
    4B8B, 4B8C, 4B8A, 4B89

  • PubMed Abstract: 
  • Shortening eukaryotic poly(A) tails represses mRNA translation and induces mRNA turnover. The major cytoplasmic deadenylase, the Ccr4-Not complex, is a conserved multisubunit assembly. Ccr4-Not is organized around Not1, a large scaffold protein that recruits two 3'-5' exoribonucleases, Caf1 and Ccr4 ...

    Shortening eukaryotic poly(A) tails represses mRNA translation and induces mRNA turnover. The major cytoplasmic deadenylase, the Ccr4-Not complex, is a conserved multisubunit assembly. Ccr4-Not is organized around Not1, a large scaffold protein that recruits two 3'-5' exoribonucleases, Caf1 and Ccr4. We report structural studies showing that the N-terminal arm of yeast Not1 has a HEAT-repeat structure with domains related to the MIF4G fold. A MIF4G domain positioned centrally within the Not1 protein recognizes Caf1, which in turn binds the LRR domain of Ccr4 and tethers the Ccr4 nuclease domain. The interactions that form the nuclease core of the Ccr4-Not complex are evolutionarily conserved. Their specific disruption affects cell growth and mRNA deadenylation and decay in vivo in yeast. Thus, the N-terminal arm of Not1 forms an extended platform reminiscent of scaffolding proteins like eIF4G and CBP80, and places the two nucleases in a pivotal position within the Ccr4-Not complex.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLY(A) RIBONUCLEASE POP2A, C, E, F288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: POP2CAF1YNR052CN3470
EC: 3.1.13.4
Find proteins for P39008 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P39008
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GENERAL NEGATIVE REGULATOR OF TRANSCRIPTION SUBUNIT 1B, G, H, I249Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CDC39NOT1ROS1YCR093WYCR1151YCR93W
Find proteins for P25655 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25655 
Go to UniProtKB:  P25655
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSE-REPRESSIBLE ALCOHOL DEHYDROGENASE TRANSCRIPTIONAL EFFECTORD, J, K, L727Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CCR4YAL021CFUN27
EC: 3.1.13.4
Find proteins for P31384 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31384 
Go to UniProtKB:  P31384
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.65α = 89.47
b = 122.911β = 89.74
c = 126.421γ = 64.22
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2012-08-26 
  • Released Date: 2012-11-21 
  • Deposition Author(s): Basquin, J., Conti, E.

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Derived calculations, Other